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Nextstrain repository for yellow fever virus

This repository contains three workflows for the analysis of yellow fever virus data:

  • ingest/ - Download data from GenBank, clean and curate it
  • phylogenetic/ - Filter sequences, align, construct phylogeny, and export for visualization
  • nextclade/ - Create nextclade datasets

Each workflow directory contains a README.md file with more information. The results of running both workflows are publicly visible at nextstrain.org/yellow-fever.

Installation

Follow the standard installation instructions for Nextstrain's suite of software tools.

Quick start

Run the phylogenetic workflow by executing the following commands in the repository checkout, after installing nextstrain per the above instructions:

cd phylogenetic/
nextstrain build .
nextstrain view .

Further documentation is available at "Running a pathogen workflow".

Working on this repository

This repository is configured to use pre-commit to help automatically catch common coding errors and syntax issues with changes before they are committed to the repo.

If you will be writing new code or otherwise working within this repository, please do the following to get started:

  1. install pre-commit, by running either python -m pip install pre-commit or brew install pre-commit, depending on your preferred package management solution
  2. install the local git hooks by running pre-commit install from the root of the repository
  3. when problems are detected, correct them in your local working tree before committing them.

Note that these pre-commit checks are also run in a GitHub Action when changes are pushed to GitHub, so correcting issues locally will prevent extra cycles of correction.